Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ep3b2 --------CCCCCCCCCEEEEEEEHHHCHHHHHHHHHHHHCC-------CEEEEEEEECCHH-HCCCHHHHH--CCC-----------CEEEEEEECCCCCC--------EECCH-HHHHHHCCC-----------CCCEEEEECCH-HHHHHHHHHCCCC--CCEEEECCCCCCCCCCCC-CCCEEEECCEEEEEEECCCCCCEECCCCCCC >P1;d1f20a2 ------CCCCCC-CCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCHHHHH-HHHH-------CC-CEEEEEEEECCC----CC----CCCCCH-HHHHHH-HCHHHHH-HHHHCCCCEEEEEECH-HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEE-C----CC--------------- >P1;d1fdra2 ----------CCCC-CCEEEEEEEHHHHHHHHHHHHHCCCCC-----CCCEEEEEEEECCHH-HCCCHHHHH-HHHHH------CCCC-EEEEEEECCC-----CCCCEEE-CCH-HHHHHCCHHHHHHCC-CCCCCCEEEEEEECH-HHHHHHHHHHHHHHCCCCC-CC----------CCCCCEEEEE-CC-------------------- >P1;d1krha2 -----------CCCCCCCEEEEEEHHHHHHHHHHHHHHHH-H----CCCCCEEEEEEECCHH-HCCCHHHHH-HHHH-------HCC-CEEEEEEECCCCCC-----CC-EECCC-HHHCC-----HHHH---HHHC-CEEEEEEEH-HHHHHHHHHHHHH-CCC----------------CC-EEEEEE-ECCC------------------ >P1;d1qfja2 CCCC-----------CCCEEEEEECCCHHHHHHHHHHHHH-H----CCCCCEEEEEEECCHH-HCCCHHHHH-HHHH-------HCC-CEEEEEEECCCCCCC----CC-EECCH-HHHHH-----HHCC---CCCC-CEEEEECCH-HHHHHHHHHHHHHCCCC----------------HHH-EECC-HHHHC------------------ >P1;d1tvca2 --------CCCCCCCCCCEEEEEECCCCHHHHHHHHHHHH-----HCCCCCEEEEEECCCCC-CCCCHHHHH-HHHH-------HCC-CCEEEECCCC----CCCCCCCCCCCCC--HHHH-----HHHHHCCCC---CEEEEECCH-HHHHHHHHHHHHH-CCCCC-----------------CCEEEC-CCCCCCC--------------- >P1;d2piaa2 -----CCCCCCCCC---EEEEEEEHHHHHHHHHHHHHHHHHC------CCEEEEEEEECCHH-HCCCHHHHHCCCCC-----------C-CEEEEECCC-CC--------CCCCC-HHHHHCCCC-----------CCEEEEEECCH-HHHHHHHHHCCCCCCCCEEEE-------------------------------------------- >P1;d2qdxa2 ---------CCCCCCCCEEEEEEEHHHHHHHHHHCCCHHHHH-----HCCEEEEEEEECCHH-HCCCHHHHHCCHHHCCCCHHHHHHH-EEEEEEECCC-----CCC--CC-CCH-HHHHHHCHHHHHHCCCCCCCCCEEEEEEECH-HHHHHHHHHHHHC-CCCCCCCC----------CCCCCEEEEE-CC--CCC--------------- >P1;d2rc5a2 ---------CCCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCC--CCCCCCCEEEEEEECCHH-HCCCHHHHH-HHHH-------HC--CEEEEEEECCC----CCCCCCCCCCCH-HHHHHH--CHHHHH-HHHH-HCCEEEEEECCCCCHHHHHHHHHHHHC-C-CCC---HHHHHHHHHHCCCEEEEE-C--------------------- >P1;d3lo8a2 -------CCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEECCHH-HCCCHHHHH-HHHH-------HCCCCEEEEEEECCC------------CCCH-HHHHHH--CHHHHH-HHHH-CCCEEEEEEE-HHHHHHHHHHHHHHHHHC-CCC---HHHHHHHHHHCCCEEEEE-E--------------------- >P1;d3ozua3 -----------CCCCCCCEEEEECCCCHHHHHHHHHHHCCC------CCCCEEEEEEECCCC-CCHHHHHHH-HHHH-------HCC-CEEEEEEECCCCCCCCCCCCCCEECCCCHHHHH-----HHHC---CC--CCEEEEECCH-HHHHHHHHHHHCC-CCC----------------HHH-EEECCCCCCCCCC--------------- >P1;d3qfta2 --------CCCC-CCCCCEEEECCHHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEEECCCCCCCCCHHHHH-HHHH-------CC-CCCEEEEEECCC----CC-----CCCCH-HHHHHH--CHHHHH-HHHH-CCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEE-E-----C--------------- >P1;d3w5ha2 CEEEECCCCCCEEEECCEEEEEEEHHHHHHHHHHHHHHHCCC----CCCCEEEEEEEECCHH-HCCCHHHHH-HHHH-------HHCCCEEEEEEECCCCCCC----CC-EECCCCHHHHH-----HHCC---CHHHCCEEEEECCH-HHHHHCCHHHHHHHCCC----------------HHH-CEEC------------------------ >P1;d4eh1a2 -----------CCCCCCCEEEEEEHHHHHHHHHHHHHHHH-C----CC-CCEEEEEEECCHH-HCCCHHHHH-HHHH-------HHC--CEEEEEECCCCCC-----CC-EECCCCCCCCC--------C---CCCC-CEEEEEECH-HHHHHHHHHHHHH-CCC----------------HHH-EEEEE-CCC------------------- >P1;d5tr9a2 ----------CCCCCCCEEEEEEEHHHHHHHHHHHCCHHHHH-----HCCEEEEEEEECCHH-HCCCHHHHH-HHCC----------C-EEEEEEECCC-----CCCCCEECCCH-HHHHHCCHHHHHHC--CCCCCCEEEEEEECH-HHHHHHHHHHHHC-CCCCC-CC----------CCCCCEEEEE-CC-------------------- PSA >P1;d1ep3b2 --------53b7065814000001790045036104502926-------0400000107358-615229405--818-----------30604000460546--------48380-4600a71a2-----------a0400000078-91064005427a1--820002273a36348074-5404370486796301005205404535014 >P1;d1f20a2 ------919108-73611000001880052037005502502565a3a034000000152286305458405-5036-------48-005312101261----6a----785450-120025-6026401-6004567010000077-810730260026001630837896045106704775200143-4----7e--------------- >P1;d1fdra2 ----------9614-2500000028a007300840571790a-----407100000116539-508537205-70475------1992-0311000144-----92bb014-470-270075750184061-504382000200041-7106401710765270561-48----------7570203163-38-------------------- >P1;d1krha2 -----------17906210000005900630272066029-7----6093302000006537-416139406-704a-------618-10302100170949-----91-57470-2a204-----9701---5a37-000000044-7205703820985-919----------------03-623373-35bd------------------ >P1;d1qfja2 6a39-----------9120000037a10930582046108-6----5581701000126437-506308704-7229-------717-507011004719bb0----61-36870-16002-----631c---5037-100002085-82066029402652905----------------672-0108-00775------------------ >P1;d1tvca2 --------8014266622000000085066026307a018-----55160301000001344-817476515-6157-------825-5070390049----0638140033550--6503-----820667603---400000005-1015003702962-80819-----------------321645-2953009--------------- >P1;d2piaa2 -----b18049a07---1000000791052007004603848------81904000106239-90543a4045a707-----------8-304021464-48--------96817-056105826-----------93110001067-9114505730a506ba11325-------------------------------------------- >P1;d2qdxa2 ---------1920581510000038a0064018104454007-----20630000010644a-5076583047701748810a40571-0200000244-----916--25-670-0410575500730916804283000100033-9108502700572-80940389----------9531102386-06--48a--------------- >P1;d2rc5a2 ---------00b96181100000269007302a203300366--608070700000103459-50651b306-4039-------71--30501101154----380827785050-211043--238204-6009-880100010388611570041017029-6-a58---287027803947103180-5--------------------- >P1;d3lo8a2 -------0b023a6381100000258007203900330035826a0605120000000365a-41443b205-4048-------546a30301200075------------5260-241035--226500-7304-9701000008-6b0074047006400852-a36---097027505969002261-5--------------------- >P1;d3ozua3 -----------879374100000000138201840650058------761500000004027-656015404-9028-------74a-306110001623880758700425650507504-----7203---18--6010200015-7006501730381-a19----------------6a3-0438523861720--------------- >P1;d3qfta2 --------910a-7251200000288006301810660061375-968034000000054296404559606-6258-------66-004302002144----3b-----85240-142037--339301-8004-950200000527610550151005002510928696026206703888204272-5-----b--------------- >P1;d3w5ha2 1624256958375360a1000000790062019204700857----828020200010843a-405337402-5038-------6379104030004823ac0----81-26480538005-----5200---41967000002058-61167103300760704----------------193-0444------------------------ >P1;d4eh1a2 -----------07439340000018700630081055018-6----91-9a01000103169-514348505-5118-------62b--082300055474c-----b0-5566070871b--------0---2288-000100036-b105402720483-807----------------881-02673-40a------------------- >P1;d5tr9a2 ----------48055621000001890064017206583048-----305100000003539-50733a505-8424----------5-0200000173-----90961237440-05006562038309--306494000200043-7006301600483-80522-6b----------9670202286-19-------------------- Translating the sequences --------**CCCCCCC*EEEEEEHHH*HHHHHHHHHHH***-------C*EEEEEEECCHH-HCCCHHHHH--***-----------*EEEEEEECCC***--------**CC*-HHHHH****-----------CCCEEEEE*CH-HHHHHHHHH****--CC****************-***EEEE************************ ------****CC-CCCC*EEEE**HHHHHHHHHHHHHHH********CCC*EEEEEEECC****CCCHHHHH-HHHH-------**-**EEEEEEECCC----**----***CC*-HHHHH*-***HH**-*****CCCEEEEE*CH-HHHHHHHHHHHH*************************EEEE*-*----**--------------- ----------CCCC-CC*EEEEEEHHHHHHHHHHHHH*****-----CCC*EEEEEEECCHH-HCCCHHHHH-HHHH*------****-EEEEEEECCC-----*******-CC*-HHHHH*****HH***-****CC*EEEEE*CH-HHHHHHHHHHHH**CCC**-**----------*****EEEE*-**-------------------- -----------CCCCCC*EEEEEEHHHHHHHHHHHHHHH*-*----*CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------***-*EEEEEEECCC***-----**-**CC*-HHH**-----HH**---***C-CEEEEE**H-HHHHHHHHHHHH*-CCC----------------**-*EEEE*-****------------------ ****-----------CC*EEEEEE***HHHHHHHHHHHH*-*----*CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------***-*EEEEEEECCC****----**-**CC*-HHHHH-----HH**---***C-CEEEEE*CH-HHHHHHHHHHHH**CCC----------------***-EE**-*****------------------ --------**CCCCCCC*EEEEEE****HHHHHHHHHHH*-----**CCC*EEEEEE*CC**-*CCCHHHHH-HHHH-------***-**EEEE**CC----**********CC*--HHHH-----HH*******---CEEEEE*CH-HHHHHHHHHHHH*-CCC**-----------------**EEE*-*******--------------- -----*****CCCC---*EEEEEEHHHHHHHHHHHHHHH***------CC*EEEEEEECCHH-HCCCHHHHH*****-----------*-*EEEEECCC-**--------**CC*-HHHHH****-----------CC*EEEEE*CH-HHHHHHHHH*****CCC****-------------------------------------------- ---------*CCCCCCC*EEEEEEHHHHHHHHHH***HH***-----*CC*EEEEEEECCHH-HCCCHHHHH**HHH***********-EEEEEEECCC-----***--**-CC*-HHHHH*****HH********CC*EEEEE*CH-HHHHHHHHHHHH*-CCC*****----------*****EEEE*-**--***--------------- ---------*CCCCCCC*EEEEEEHHHHHHHHHHHHHHH***--***CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------**--*EEEEEEECCC----*********CC*-HHHHH*--**HH**-****-*CCEEEEE*C****HHHHHHHHHH**C-C-***---*************EEEE*-*--------------------- -------***CCCCCCC*EEEEEEHHHHHHHHHHHHHHH********CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------*****EEEEEEECCC------------*CC*-HHHHH*--**HH**-****-CCCEEEEE**-*HHHHHHHHHHHH****C-***---*************EEEE*-*--------------------- -----------CCCCCC*EEEEE****HHHHHHHHHHH***------CCC*EEEEEEECC**-*C**HHHHH-HHHH-------***-*EEEEEEECCC*************CC**HHHHH-----HH**---**--CCEEEEE*CH-HHHHHHHHHHH**-CCC----------------***-EEE**********--------------- --------**CC-CCCC*EEEE**HHHHHHHHHHHHHHH*****-**CCC*EEEEEEECC****CCCHHHHH-HHHH-------**-***EEEEEECCC----**-----**CC*-HHHHH*--**HH**-****-CCCEEEEE*****HHHHHHHHHHH*************************EEEE*-*-----*--------------- **********C****CC*EEEEEEHHHHHHHHHHHHHHH***----*CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------*****EEEEEEECCC****----**-**CC**HHHHH-----HH**---****CCEEEEE*CH-HHHHH**HHHHH**CCC----------------***-*EE*------------------------ -----------CCCCCC*EEEEEEHHHHHHHHHHHHHHH*-*----*C-C*EEEEEEECCHH-HCCCHHHHH-HHHH-------***--*EEEEEECCC***-----**-**CC*******--------*---***C-CEEEEE*CH-HHHHHHHHHHHH*-CCC----------------***-EEEE*-***------------------- ----------CCCCCCC*EEEEEEHHHHHHHHHHH**HH***-----*CC*EEEEEEECCHH-HCCCHHHHH-HH**----------*-EEEEEEECCC-----********CC*-HHHHH*****HH**--****CC*EEEEE*CH-HHHHHHHHHHHH*-CCC**-**----------*****EEEE*-**-------------------- 52343.tem _________________________________ --------**CCCCCCC*EEEEEEHHHHHHHHHHHHHHH***---**CCC*EEEEEEECCHH-HCCCHHHHH-HHHH-------*****EEEEEEECCC***-*********CC*-HHHHH*****HH**-*****CCCEEEEE*CH-HHHHHHHHHHHH**CCC*****--*************EEEE*-****-**--------------- Structural block scores 0 7 - 4.6 H 75.0 57.5 75.0 75.0 41.1 75.0 49.4 75.0 75.0 65.6 75.0 75.0 4.4 75.0 75.0 8 9 * 3.2 M 4.0 5.0 75.0 75.0 75.0 4.0 2.0 38.0 37.5 5.8 75.0 5.0 6.5 75.0 75.0 10 16 C 4.6 H 5.5 14.3 14.6 14.3 55.0 3.9 35.9 4.3 5.2 4.8 16.1 14.4 4.9 14.4 4.3 18 23 E 4.9 H 0.2 0.2 0.3 0.0 0.5 0.0 0.0 0.5 0.3 0.3 0.0 0.3 0.0 0.2 0.2 24 38 H 4.8 H 3.1 3.0 4.0 3.2 3.8 3.6 2.9 3.7 3.0 2.7 2.5 3.1 3.1 2.9 3.9 39 41 * 1.7 P 5.7 2.3 6.5 30.3 29.7 52.7 6.7 2.3 5.0 5.3 29.3 3.3 6.7 29.7 4.0 42 44 - 4.5 M 75.0 5.3 75.0 75.0 75.0 75.0 75.0 75.0 52.0 6.2 75.0 29.0 75.0 75.0 75.0 45 46 * 3.5 M 75.0 6.8 75.0 40.5 40.0 5.0 75.0 75.0 4.0 3.0 75.0 7.5 41.5 42.0 75.0 47 49 C 4.7 H 50.0 4.5 3.7 4.0 4.7 2.3 28.0 2.7 2.3 2.0 4.7 3.7 3.3 28.3 2.7 51 57 E 5.0 H 0.1 0.1 0.3 0.3 0.6 0.1 0.7 0.1 0.1 0.0 0.0 0.0 0.4 0.3 0.0 58 59 C 5.0 H 5.0 3.5 5.5 5.5 5.0 2.0 4.0 5.0 3.5 4.5 2.0 4.5 6.0 2.0 4.0 60 61 H 4.2 M 6.5 5.0 6.0 5.0 5.0 4.0 6.0 7.2 7.0 7.8 4.5 5.5 6.8 7.5 6.0 64 66 C 4.9 H 2.7 3.0 4.3 2.7 3.0 4.0 3.0 4.3 3.7 3.0 3.7 3.0 2.7 2.7 3.3 67 71 H 5.0 H 4.0 4.4 3.4 4.4 3.8 4.8 4.3 4.0 4.3 4.3 2.8 5.2 3.2 4.4 4.7 73 76 H 4.5 M 23.0 3.5 4.5 5.4 5.0 4.8 6.1 3.8 4.0 4.0 4.8 5.2 4.0 3.8 4.5 77 83 - 4.8 H 75.0 75.0 65.0 75.0 75.0 75.0 75.0 5.1 75.0 75.0 75.0 75.0 75.0 75.0 75.0 84 88 * 2.6 P 60.6 17.4 19.2 18.2 19.0 19.0 61.6 17.6 32.2 5.7 19.9 17.4 5.2 33.9 61.0 89 95 E 4.8 H 1.4 1.9 0.7 0.9 1.3 2.7 12.1 0.3 1.1 0.9 1.1 1.6 1.0 1.9 0.3 96 98 C 4.9 H 3.3 3.0 3.0 2.7 4.0 29.3 4.7 3.3 3.3 4.0 3.0 3.0 4.7 4.7 3.7 99 101 * 3.6 M 5.0 75.0 75.0 7.3 10.7 75.0 29.0 75.0 75.0 75.0 6.3 75.0 8.7 7.8 75.0 103 111 * 3.1 M 59.7 37.4 21.0 44.1 43.4 3.1 60.0 35.9 5.3 67.2 4.2 44.7 43.6 44.1 12.4 112 113 C 5.0 H 5.5 4.5 5.5 5.5 7.5 5.0 4.5 6.5 2.5 4.0 5.5 3.0 6.0 6.0 4.0 116 120 H 4.7 H 4.1 1.0 3.2 3.7 1.8 17.8 2.4 2.0 1.6 2.0 3.2 2.0 3.2 5.5 2.2 121 125 * 3.5 M 19.1 17.6 3.6 75.0 75.0 75.0 19.2 3.4 31.6 31.8 75.0 32.6 75.0 75.0 3.2 126 127 H 4.6 H 75.0 5.0 6.0 8.0 4.5 5.0 75.0 5.0 5.0 5.5 4.5 6.0 3.5 75.0 5.5 128 129 * 1.9 P 75.0 0.5 3.0 0.5 6.8 3.0 75.0 4.5 2.0 0.0 1.5 0.5 0.0 37.5 4.5 131 135 * 2.8 P 75.0 3.0 17.4 33.7 31.6 18.2 75.0 4.0 18.0 17.8 46.8 17.4 32.8 32.4 17.6 136 138 C 4.4 M 4.8 4.3 3.3 27.3 27.7 51.3 4.3 3.7 5.3 5.3 27.0 4.7 4.3 27.7 4.3 139 143 E 5.0 H 0.0 0.2 0.4 0.0 0.4 0.0 0.4 0.2 0.4 0.2 0.6 0.4 0.4 0.2 0.4 148 159 H 4.8 H 4.0 2.9 3.3 4.2 3.8 2.8 4.2 3.7 2.8 3.6 3.3 2.4 2.9 3.7 2.9 160 161 * 2.1 P 38.0 0.0 3.5 40.0 3.5 38.5 3.0 38.5 1.0 0.0 38.0 0.0 3.0 39.0 39.0 162 164 C 4.4 M 28.3 3.3 4.0 6.3 4.7 5.3 7.7 5.7 30.0 5.0 6.8 2.7 3.7 5.0 4.3 165 169 * 3.3 M 0.8 5.2 18.8 75.0 75.0 47.0 17.2 4.8 34.7 33.9 75.0 5.0 75.0 75.0 19.3 170 171 - 4.5 M 5.0 7.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.5 75.0 75.0 75.0 172 184 * 3.4 M 10.0 3.7 47.8 58.4 58.8 69.5 75.0 47.6 4.5 4.5 59.2 4.0 58.7 59.0 48.0 185 188 E 4.6 H 3.5 1.2 2.5 3.8 2.2 3.2 75.0 3.2 3.0 2.5 3.8 3.2 3.0 3.8 3.0 191 194 * 3.1 M 7.0 57.2 40.2 8.2 4.8 4.8 75.0 39.0 57.5 57.5 4.5 57.5 75.0 22.4 40.0 196 197 * 3.9 M 0.5 10.8 75.0 75.0 75.0 4.5 75.0 9.2 75.0 75.0 1.0 43.2 75.0 75.0 75.0 198 212 - 4.8 H 2.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>